A common assumption about how to do science is that it requires methodological naturalism. However, specifying what natural means is not as easy as it initially appears. In this paper, I examine the validity of methodological naturalism in light of the various ways by which the term 'natural' can be understood: a) natural as material, b) natural as physical, and c) natural as created by God. One major reason that methodological naturalism has currently taken center stage is that it is utilized to criticize the scientific legitimacy of Intelligent Design theory. Thus, when relevant, these different understandings of what natural means are examined in light of how successful they are in precluding the theory of intelligent design from becoming a legitimate scientific theory. I conclude by noting that none of these various meanings of natural, when deployed in support of methodological naturalism, are successful in regarding ID theory as unscientific.